FISICO: Fast Image SegmentatIon COrrection.

BACKGROUND AND PURPOSE In clinical diagnosis, medical image segmentation plays a key role in the analysis of pathological regions. Despite advances in automatic and semi-automatic segmentation techniques, time-effective correction tools are commonly needed to improve segmentation results. Therefore, these tools must provide faster corrections with a lower number of interactions, and a user-independent solution to reduce the time frame between image acquisition and diagnosis. METHODS We present a new interactive method for correcting image segmentations. Our method provides 3D shape corrections through 2D interactions. This approach enables an intuitive and natural corrections of 3D segmentation results. The developed method has been implemented into a software tool and has been evaluated for the task of lumbar muscle and knee joint segmentations from MR images. RESULTS Experimental results show that full segmentation corrections could be performed within an average correction time of 5.5±3.3 minutes and an average of 56.5±33.1 user interactions, while maintaining the quality of the final segmentation result within an average Dice coefficient of 0.92±0.02 for both anatomies. In addition, for users with different levels of expertise, our method yields a correction time and number of interaction decrease from 38±19.2 minutes to 6.4±4.3 minutes, and 339±157.1 to 67.7±39.6 interactions, respectively.

Small sample confidence intervals for the mean of a positively skewed distribution

This thesis proposes some confidence intervals for the mean of a positively skewed distribution. The following confidence intervals are considered: Student-t, Johnson-t, median-t, mad-t, bootstrap-t, BCA, T1 , T3 and six new confidence intervals, the median bootstrap-t, mad bootstrap-t, median T1, mad T1 , median T3 and the mad T3. A simulation study has been conducted and average widths, coefficient of variation of widths, and coverage probabilities were recorded and compared across confidence intervals. To compare confidence intervals, the width and coverage probabilities were compared so that smaller widths indicated a better confidence interval when coverage probabilities were the same. Results showed that the median T1 and median T3 outperformed other confidence intervals in terms of coverage probability and the mad bootstrap-t, mad-t, and mad T3 outperformed others in terms of width. Some real life data are considered to illustrate the findings of the thesis.

Escala diagramática e influência de sistemas de produção na ocorrência do crestamento gomoso da melancia

CHAPTER 1 - The gummy stem blight, caused by the fungus D. bryoniae, is a disease commonly found in watermelon cultivated in several countries. In Brazil, there are numerous studies related to the disease, but there are not uniform methods for quantifying of disease severity in the field. Thus, we developed a diagrammatic scale based on scanned photos of watermelon leaves infected with D. bryoniae. The scale developed showed levels of 0; 10; 20; 45; 65 and 90% of severity. The scale validation was divided into two parts: initially, 10 evaluators (half with experienced and other half without experience) estimated the disease severity based on the initial observation of 100 photos of watermelon leaves with symptoms of the disease at different severity levels. Before, the same evaluators estimated the disease severity with the support of the scale prepared from the Quant program. Data were analyzed using linear regression and were obtained angular, linear, and correlation coefficients. Based on these data, we determined the accuracy and precision of the evaluations. The correlation coefficients (R2) ranged from 0.88 - 0.97 for the experienced evaluators and from 0.55 - 0.95 for the inexperienced evaluators. The average angular coefficient (A) for inexperienced evaluators was 20.42 and 8.61 with and without the support of diagrammatic scale, respectively. Experienced evaluators showed values of average linear coefficient of 5.30 and 1.68 with and without the support of diagrammatic scale, respectively. The absolute errors analysis indicated that the use of diagrammatic scale contributed to minimize the flaws in the severity levels estimation. The diagrammatic scale proposed shown adequate for gummy stem blight severity evaluation in watermelon. CHAPTER 2 - The gummy stem blight (Didymella bryoniae) is a disease that affects the productivity of watermelon leading to losses over 40%. This study aimed to evaluate the efficiency of different production systems in control of gummy stem blight in watermelon for to establish efficient methods to combat the disease. There were applied the following treatments: conventional tillage (T1), integrated management (T2) and organic management (T3). In T1 and T2 were applied mineral fertilization and T3 was used bovine manure. There was application of fungicides and insecticides in commercial dose in T1 and T2, being after soil chemical analysis in T2. Disease severity was assessed by grading scale. The experimental design was randomized blocks. The severity of gummy stem blight has increased substantially during the fruit formation. Watermelon plants grown with integrated management (T2) showed lower levels of disease severity, while plants in organic management (T3) exhibited higher levels of severity. We conclude that management based on judicious accompaniments in field represents best way to achieve the phytosanitary aspect adequate for cultivation of watermelon in Tocantins.

Lake–atmosphere interactions at Alqueva reservoir: a case study in the summer of 2014

The study of lake–atmosphere interactions was the main purpose of a 2014 summer experiment at Alqueva reservoir in Portugal. Near-surface fluxes of momentum, heat and mass [water vapour (H2O) and carbon dioxide (CO2)] were obtained with the new Campbell Scientific’s IRGASON Integrated Open-Path CO2/H2O Gas Analyser and 3D Sonic Anemometer between 2 June and 2 October. On average, the reservoir was releasing energy in the form of sensible and latent heat flux during the study period. At the end of the 75 d, the total evaporation was estimated as 490.26 mm. A high correlation was found between the latent heat flux and the wind speed (R = 0.97). The temperature gradient between air and water was positive between 12 and 21 UTC, causing a negative sensible heat flux, and negative during the rest of the day, triggering a positive sensible heat flux. The reservoir acted as a sink of atmospheric CO2 with an average rate of −0.026 mg m−2 s−1. However, at a daily scale we found an unexpected uptake between 0 and 9 UTC and almost null flux between 13 and 19 UTC. Potential reasons for this result are further discussed. The net radiation was recorded for the same period and water column heat storage was estimated using water temperature profiles. The energy balance closure for the analysed period was 81%. In-water solar spectral downwelling irradiance profiles were measured with a new device allowing measurements independent of the solar zenith angle, which enabled the computation of the attenuation coefficient of light in the water column. The average attenuation coefficient for the photosynthetically active radiation spectral region varied from 0.849 ± 0.025 m−1 on 30 July to 1.459 ± 0.007 m−1 on 25 September.

Low relatedness among cooperatively breeding workers of the greenhead ant Rhytidoponera metallica

The greenhead ant Rhytidoponera metallica has long been recognized as posing a potential challenge to kin selection theory because it has large queenless colonies where apparently many of the morphological workers are mated and reproducing. However this species has never been studied genetically and important elements of its breeding system and kin structure remain uncertain. We used microsatellite markers to measure the relatedness among nestmates unravel the fine-scale population genetic structure and infer the breeding system of R. metallica. The genetic relatedness among worker nestmates is very low but significantly greater than zero (r = 0.082 +/- 0.015) which demonstrates that nests contain many distantly related breeders. The inbreeding coefficient is very close to and not significantly different from zero indicating random mating and lack of microgeographic genetic differentiation. On average. closely located nests are not more similar genetically than distant nests which is surprising as new colonies form by budding and female dispersal is restricted. Lack of inbreeding and absence of population viscosity indicates high gene flow mediated by males. Overall the genetic pattern detected in R. metallica suggests that a high number of moderately related workers mate with unrelated males from distant nests. This breeding system results in the lowest relatedness among nestmates reported for social insect species where breeders and helpers are not morphologically differentiated. [References: 69]

Genetic analysis of average annual productivity of Nellore breeding cows (COWPROD)

With the aim of estimating the coefficient of heritability of average annual productivity of Nellore cows (COWPROD), a data set from 24,855 animals with known pedigree was analyzed. COWPROD is defined as the amount (in kilograms) of weaned calves produced yearly by one cow during her remaining time in herd ignoring a fixed period of 365 days. COWPROD was calculated regarding three standards: a) based on the post-weaning weight from the calves ignoring any kind of adjustment (COWPROD_NAJ), b) adjusted weight for the fixed effects (COWPROD_AJFIX) and c) adjusted weight for the fixed effects and for the genetic merit of the sire (COWPROD_AJFIN). The obtained heritabilities were 0.15, 0.15 and 0.16 for COWPROD_NAJ, COWPROD_AJFIX and COWPROD_AJFIN, respectively. A complete set composed of 105,158 COWPROD records on 130,740 animals in pedigree was also analyzed for predicting the genetic merit of all animals in the data set and for the calculation of the genetic, phenotypic and residual trends. Ranking correlation was high for the adjusted and non-adjusted data, yet, for some of the animals, the difference among the genetic values was large. This would be an indication that it would be better to work always with the adjusted weaning weights. The genetic trend was positive, but was of small magnitude (0.26% of the trait average) and the residual trend was negative as a consequence of the large intensification of the production system, which has been occurring in the last years in the farms studied. The phenotypic trend was also negative and intermediate between the genetic and the residual ones.

Friction coefficient and abrasive wear modes in ball-cratering tests conducted at constant normal force and constant pressure-Preliminary results

The micro-scale abrasive wear test by rotative ball has gained large acceptance in universities and research centers, being widely used in studies on the abrasive wear of materials. Two wear modes are usually observed in this type of test: ""rolling abrasion"" results when the abrasive particles roll on the surface of the tested specimen, while ""grooving abrasion"" is observed when the abrasive particles slide; the type of wear mode has a significant effect on the overall behaviour of a tribological system. Several works on the friction coefficient during abrasive wear tests are available in the literature, but only a few were dedicated to the friction coefficient in micro-abrasive wear tests conducted with rotating ball. Additionally, recent works have identified that results may also be affected by the change in contact pressure that occurs when tests are conducted with constant applied force. Thus, the purpose of this work is to study the relationship between friction coefficient and abrasive wear modes in ball-cratering wear tests conducted at ""constant normal force"" and ""constant pressure"". Micro-scale abrasive wear tests were conducted with a ball of AISI52100 steel and a specimen of AISIH10 tool steel. The abrasive slurry was prepared with black silicon carbide (SiC) particles (average particle size of 3 mu m) and distilled water. Two constant normal force values and two constant pressure values were selected for the tests. The tangential and normal loads were monitored throughout the tests and their ratio was calculated to provide an indication of the friction coefficient. In all cases, optical microscopy analysis of the worn craters revelated only the presence of grooving abrasion. However, a more detailed analysis conducted by SEM has indicated that different degrees of rolling abrasion have also occurred along the grooves. The results have also shown that: (i) for the selected values of constant normal force and constant pressure, the friction coefficient presents, approximately, the same range of values and (ii) loading conditions play an important role on the occurrence of rolling abrasion or grooving abrasion and, consequently, on the average value and scatter of the friction coefficient in micro-abrasive wear tests. (C) 2009 Elsevier B.V. All rights reserved.

Apparent digestibility coefficient of protein and amino acids of acid, biological and enzymatic silage for Nile tilapia (Oreochromis niloticus)

Using the fish silage to partially replace proteic feedstuff in aquafeeds is an alternative to mitigate sanitary and environmental problems caused by the lack of adequate destination for fisheries residues. It would also lower feed costs, consequently improving fish culture profitability. However, using fish silages in aquafeeds depends on determination of its apparent digestibility coefficients (ADC). This work aimed to determining the ADC of crude protein and amino acids of acid silage (AS), biological silage (BS) and enzymatic silage (ES) for juvenile Nile tilapia (94.5 +/- 12.7 g). The ADC(CP) was: 92.0%, 89.1% and 93.7% for AS, BS and SE respectively. The average ADC of amino acids was: 91.8%, 90.8% and 94.6% for AS, BS and ES respectively. Results encourage the use of AS, BS and ES to partially replace protein sources in balanced diets for neotropical fish.

Genetic characterization of ninety elite soybean cultivars using coefficient of parentage

The objective of this work was to estimate the coefficient of parentage and to understand the genetic structure of 90 elite soybean cultivars, which are adapted to different Brazilian environments. A total of 4,005 coefficients of parentage (f) were obtained and used to group the cultivars by UPGMA method. The constructed dendrogram showed several related cultivar groups which shared similar ancestors and clearly showed the genetic structure of the main Brazilian cultivars. Effective population sizes (Ne) were also estimated for cultivars in different generations. The average f = 0.2124 value, obtained from cultivars classified into four decades according to the release year, suggested effective soybean population sizes of 11 and 13 calculated using arithmetic and weighted means, respectively. The relatively small Ne and the high parentage coefficient support the conclusion that there is a high similarity degree among the main soybean cultivars in Brazil.

A cophenetic correlation coefficient for Tocher's method

The objective of this work was to propose a way of using the Tocher's method of clustering to obtain a matrix similar to the cophenetic one obtained for hierarchical methods, which would allow the calculation of a cophenetic correlation. To illustrate the obtention of the proposed cophenetic matrix, we used two dissimilarity matrices - one obtained with the generalized squared Mahalanobis distance and the other with the Euclidean distance - between 17 garlic cultivars, based on six morphological characters. Basically, the proposal for obtaining the cophenetic matrix was to use the average distances within and between clusters, after performing the clustering. A function in R language was proposed to compute the cophenetic matrix for Tocher's method. The empirical distribution of this correlation coefficient was briefly studied. For both dissimilarity measures, the values of cophenetic correlation obtained for the Tocher's method were higher than those obtained with the hierarchical methods (Ward's algorithm and average linkage - UPGMA). Comparisons between the clustering made with the agglomerative hierarchical methods and with the Tocher's method can be performed using a criterion in common: the correlation between matrices of original and cophenetic distances.

Methicillin-resistant Staphylococcus aureus: phylogenetic relatedness between European epidemic clones and Swiss sporadic strains.

We have compared the phylogenetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) strains from Switzerland and their phylogenetic relationships with European epidemic clones, using multiprimer random amplification polymorphic DNA (RAPD). Strains included 24 European epidemic clones (59 strains), 66 sporadic strains isolated in Switzerland in 1996-1997, and 15 reference strains of five other Staphylococcus species. Similarity and clustering analysis with the Jaccard's coefficient showed that the maximum genetic distance between MRSA strains was 0.43, whereas the minimum genetic distance between the six Staphylococcus species was 0.97, indicating that the method permits phylogenetic hierarchization. The 24 MRSA clones reported to be epidemic in European countries during the 1990s were distributed into seven different genetic clusters with a maximum distance of 0.29 among them. This clustering pattern was confirmed by the analysis of a subset of MRSA strains by multilocus enzyme electrophoresis at 12 loci. Most of the sporadic Swiss strains were distributed into these seven different genetic clusters, together with the epidemic MRSA clones. This suggests that there is no phylogenetic cluster specific to epidemic clones of MRSA.

Guidelines for irrigation scheduling of banana crop in São Francisco Valley, Brazil. II - Water consumption, crop coefficient, and physiologycal behavior

The water consumption and the crop coefficient of the banana cv. Pacovan were estimated in Petrolina County, northeastern Brazil, in order to establish guidelines to irrigation water management. Evaluations were carried out since planting in January 1999 to the 3rd harvest in September 2001 on a microsprinkler irrigated orchard, with plants spaced in a 3 x 3 m grid. Average daily water consumption was 3.9, 4.0, and 3.3 mm in the 1st, 2nd and 3rd growing seasons, respectively. Crop coefficient values increased from 0.7 (vegetative growth) to 1.1 (flowering). Even with high soil water availability, transpiration was reduced due to high evaporative demand.

Organizational commitment and perceived relatedness as correlates of the intention to continue officiating in track and field

The objectives of the present study were to explore three components of organizational commitment (affective [AC], normative [NC] and continuance [CC] commitment; Allen & Meyer, 1991), perceived relatedness (Oeci & Ryan, 1985; 2002), and behavioural intention (Ajzen, 2002) within the context of volunteer track and field officiating. The objectives were examined in a 2-phase study. Ouring phase 1, experts (N = 10) with domain familiarity assessed the item content relevance and representation of modified organizational commitment (OC; Meyer, Allen & Smith, 1993) and perceived relatedness (La Guardia, Oeci, Ryan & Couchman, 2000) items. Fourteen of 26 (p < .05) items were relevant (Aiken's coefficient V) and NC (M = 3.88, SO = .64), CC (M = 3.63, SD = .52), and relatedness (M = 4.00, SD = .93) items had mean item content-representation ratings of either "good" or "very good" while AC (M = 2.50, SD = 0.58) was rated "fair". Participants in phase 2 (N = 80) responded to items measuring demographic variables, perceptions of OC to Athletics Canada, perceived relatedness to other track and field officials, and a measure of intention (yiu, Au & Tang, 2001) to continue officiating. Internal consistency reliability estimates (Cronbach's (1951) coefficient alpha) were as follows: (a) AC = .78, (b) CC = .85, (c) NC = .80 (d) perceived relatedness = .70 and, (e) intention = .92 in the present sample. Results suggest that the track and field officials felt only minimally committed to Athletics Canada (AC M = 3.90, SD = 1.23; NC M = 2.47, SD = 1.25; CC M = 3.32; SD = 1.34) and that their relationships with other track and field officials were strongly endorsed (M = 5.86, SD = 0.74). Bivariate correlations (Pearson r) indicated that perceived relatedness to other track and field officials demonstrated the strongest relationship with intention to continue officiating (r = .346, p < .05), while dimensions of OC were not significantly related to intention (all p's > .05). Together perceived relatedness (j3 = .339, p = .004), affective commitment (j3 = -.1 53, p = .308), normative commitment (j3 = -.024, p = .864) and continuance commitment (j3 = .186, P = .287) contribute to the prediction of intention to continued officiating (K = .139). These relationships remained unaffected by the inclusion of demographic (j3age = -.02; P years with Athletics Canada = -.13; bothp's > .05) or alternative commitment (j3sport = -.19; P role = .15; Pathletes = .20; all p' s > .05) considerations. Three open-ended questions elicited qualitative responses regarding participants' reasons for officiating. Responses reflecting initial reasons for officiating formed these higher order themes: convenience, helping reasons, extension of role, and intrinsic reasons. Responses reflecting reasons for continuing to officiate formed these higher order themes: track and field, to help, and personal benefits. Responses reflecting changes that would influence continued involvement were: political, organizational/structural, and personal. These results corroborate the findings of previous investigations which state that the reasons underpinning volunteer motivations change over time (Cuskelly et al., 2002). Overall, the results of this study suggest that track and field officials feel minimal commitment to the organization of Athletics Canada but a stronger bond with their fellow officials. Moreover, the degree to which track and field officials feel meaningfully connected to one another appears to exert a positive influence on their intentions to continue officiating. As such, it is suggested that in order to promote continued involvement, Athletics Canada increases its focus on fostering environments promoting positive interactions among officials.

Monthly average temperature modelling

This research is associated with the goal of the horticultural sector of the Colombian southwest, which is to obtain climatic information, specifically, to predict the monthly average temperature in sites where it has not been measured. The data correspond to monthly average temperature, and were recorded in meteorological stations at Valle del Cauca, Colombia, South America. Two components are identified in the data of this research: (1) a component due to the temporal aspects, determined by characteristics of the time series, distribution of the monthly average temperature through the months and the temporal phenomena, which increased (El Nino) and decreased (La Nina) the temperature values, and (2) a component due to the sites, which is determined for the clear differentiation of two populations, the valley and the mountains, which are associated with the pattern of monthly average temperature and with the altitude. Finally, due to the closeness between meteorological stations it is possible to find spatial correlation between data from nearby sites. In the first instance a random coefficient model without spatial covariance structure in the errors is obtained by month and geographical location (mountains and valley, respectively). Models for wet periods in mountains show a normal distribution in the errors; models for the valley and dry periods in mountains do not exhibit a normal pattern in the errors. In models of mountains and wet periods, omni-directional weighted variograms for residuals show spatial continuity. The random coefficient model without spatial covariance structure in the errors and the random coefficient model with spatial covariance structure in the errors are capturing the influence of the El Nino and La Nina phenomena, which indicates that the inclusion of the random part in the model is appropriate. The altitude variable contributes significantly in the models for mountains. In general, the cross-validation process indicates that the random coefficient model with spatial spherical and the random coefficient model with spatial Gaussian are the best models for the wet periods in mountains, and the worst model is the model used by the Colombian Institute for Meteorology, Hydrology and Environmental Studies (IDEAM) to predict temperature.

API-CALC 1.0: a computer program for calculating the average probability of identity allowing for substructure, inbreeding and the presence of close relatives

Individual identification via DNA profiling is important in molecular ecology, particularly in the case of noninvasive sampling. A key quantity in determining the number of loci required is the probability of identity (PIave), the probability of observing two copies of any profile in the population. Previously this has been calculated assuming no inbreeding or population structure. Here we introduce formulae that account for these factors, whilst also accounting for relatedness structure in the population. These formulae are implemented in API-CALC 1.0, which calculates PIave for either a specified value, or a range of values, for F-IS and F-ST.